diff options
| -rw-r--r-- | python/refcat/tasks.py | 50 |
1 files changed, 48 insertions, 2 deletions
diff --git a/python/refcat/tasks.py b/python/refcat/tasks.py index 9d4c982..07c1217 100644 --- a/python/refcat/tasks.py +++ b/python/refcat/tasks.py @@ -572,8 +572,8 @@ class BrefZipPMID(Refcat): """ def requires(self): return { - "refs": RefsDOI(), - "fatcat": FatcatDOI(), + "refs": RefsPMID(), + "fatcat": FatcatPMID(), } def run(self): @@ -587,3 +587,49 @@ class BrefZipPMID(Refcat): def output(self): return luigi.LocalTarget(path=self.path(ext="json.zst"), format=Zstd) + + +class BrefZipPMCID(Refcat): + """ + Run skate-reduce from two files. + """ + def requires(self): + return { + "refs": RefsPMCID(), + "fatcat": FatcatPMCID(), + } + + def run(self): + output = shellout(r""" + skate-reduce -m exact -r pmcid -F <(zstdcat -T0 {refs}) -L <(zstdcat -T0 {fatcat}) | + zstd -c -T0 > {output} + """, + refs=self.input().get("refs").path, + fatcat=self.input().get("fatcat").path) + luigi.LocalTarget(output).move(self.output().path) + + def output(self): + return luigi.LocalTarget(path=self.path(ext="json.zst"), format=Zstd) + + +class BrefZipArxiv(Refcat): + """ + Run skate-reduce from two files. + """ + def requires(self): + return { + "refs": RefsArxiv(), + "fatcat": FatcatArxiv(), + } + + def run(self): + output = shellout(r""" + skate-reduce -m exact -r arxiv -F <(zstdcat -T0 {refs}) -L <(zstdcat -T0 {fatcat}) | + zstd -c -T0 > {output} + """, + refs=self.input().get("refs").path, + fatcat=self.input().get("fatcat").path) + luigi.LocalTarget(output).move(self.output().path) + + def output(self): + return luigi.LocalTarget(path=self.path(ext="json.zst"), format=Zstd) |